Properly initialize idef in topologies

Adds and uses functions to properly initialize and clean up
idef structure in topologies.

This is preparing for changes that no longer use snew for
allocating topology datastructures.

Change-Id: Iabad6d95bc994f4b292c063572a6d83e7f02036d

diff --git a/src/gromacs/topology/idef.cpp b/src/gromacs/topology/idef.cpp
index 2274ef87fcdbef1510add66e35d6a01a62bd2fd6..5739cacef04a902c24d2bd984f6823edf3e0ad79 100644 (file)
--- a/src/gromacs/topology/idef.cpp
+++ b/src/gromacs/topology/idef.cpp
@@ -42,6 +42,7 @@
 
 #include "gromacs/topology/ifunc.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/txtdump.h"
 
 static void pr_harm(FILE *fp, const t_iparams *iparams, const char *r, const char *kr)
@@ -450,3 +451,40 @@ void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
         }
     }
 }
+
+void init_idef(t_idef *idef)
+{
+    idef->ntypes           = 0;
+    idef->atnr             = 0;
+    idef->functype         = nullptr;
+    idef->iparams          = nullptr;
+    idef->fudgeQQ          = 0.0;
+    idef->iparams_posres   = nullptr;
+    idef->iparams_fbposres = nullptr;
+    for (int f = 0; f < F_NRE; ++f)
+    {
+        idef->il[f].iatoms          = nullptr;
+        idef->il[f].nalloc          = 0;
+        idef->il[f].nr              = 0;
+        idef->il[f].nr_nonperturbed = 0;
+    }
+    idef->cmap_grid.cmapdata      = nullptr;
+    idef->iparams_posres_nalloc   = 0;
+    idef->iparams_fbposres_nalloc = 0;
+    idef->ilsort                  = 0;
+}
+
+void done_idef(t_idef *idef)
+{
+    sfree(idef->functype);
+    sfree(idef->iparams);
+    sfree(idef->iparams_posres);
+    sfree(idef->iparams_fbposres);
+    for (int f = 0; f < F_NRE; ++f)
+    {
+        sfree(idef->il[f].iatoms);
+    }
+
+    sfree(idef->cmap_grid.cmapdata);
+    init_idef(idef);
+}

diff --git a/src/gromacs/topology/idef.h b/src/gromacs/topology/idef.h
index 3ebb53784cd4999fbd5dfa7e9d291fe98918cd50..9059e089e41569e534b88224a4986715bed2110f 100644 (file)
--- a/src/gromacs/topology/idef.h
+++ b/src/gromacs/topology/idef.h
@@ -328,4 +328,18 @@ void pr_ffparams(FILE *fp, int indent, const char *title,
 void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
              gmx_bool bShowNumbers, gmx_bool bShowParameters);
 
+/*! \brief
+ * Properly initialize idef struct.
+ *
+ * \param[in] idef Pointer to idef struct to initialize.
+ */
+void init_idef(t_idef *idef);
+
+/*! \brief
+ * Properly clean up idef struct.
+ *
+ * \param[in] idef Pointer to idef struct to clean up.
+ */
+void done_idef(t_idef *idef);
+
 #endif

diff --git a/src/gromacs/topology/topology.cpp b/src/gromacs/topology/topology.cpp
index df6e857c57a5eda44afa86c76ec6936d5835f99a..568dbee391cad1f6c2e703dfcca4fd259a1a662b 100644 (file)
--- a/src/gromacs/topology/topology.cpp
+++ b/src/gromacs/topology/topology.cpp
@@ -100,6 +100,7 @@ void init_mtop(gmx_mtop_t *mtop)
 void init_top(t_topology *top)
 {
     top->name = nullptr;
+    init_idef(&top->idef);
     init_atom(&(top->atoms));
     init_atomtypes(&(top->atomtypes));
     init_block(&top->cgs);
@@ -170,16 +171,7 @@ gmx_mtop_t::~gmx_mtop_t()
 
 void done_top(t_topology *top)
 {
-    sfree(top->idef.functype);
-    sfree(top->idef.iparams);
-    sfree(top->idef.cmap_grid.cmapdata);
-    for (int f = 0; f < F_NRE; ++f)
-    {
-        sfree(top->idef.il[f].iatoms);
-        top->idef.il[f].iatoms = nullptr;
-        top->idef.il[f].nalloc = 0;
-    }
-
+    done_idef(&top->idef);
     done_atom(&(top->atoms));
 
     /* For GB */
@@ -197,21 +189,13 @@ void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
     {
         if (top != nullptr)
         {
-            for (int f = 0; f < F_NRE; ++f)
-            {
-                sfree(top->idef.il[f].iatoms);
-                top->idef.il[f].iatoms = nullptr;
-                top->idef.il[f].nalloc = 0;
-            }
+            done_idef(&top->idef);
             done_atom(&top->atoms);
             done_block(&top->cgs);
             done_blocka(&top->excls);
             done_block(&top->mols);
             done_symtab(&top->symtab);
             open_symtab(&mtop->symtab);
-            sfree(top->idef.functype);
-            sfree(top->idef.iparams);
-            sfree(top->idef.cmap_grid.cmapdata);
             done_atomtypes(&(top->atomtypes));
         }
 
@@ -219,23 +203,23 @@ void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
     }
 }
 
+void init_localtop(gmx_localtop_t *top)
+{
+    init_block(&top->cgs);
+    init_blocka(&top->excls);
+    init_idef(&top->idef);
+    init_atomtypes(&top->atomtypes);
+}
+
 void done_localtop(gmx_localtop_t *top)
 {
     if (top == nullptr)
     {
         return;
     }
-    sfree(top->idef.cmap_grid.cmapdata);
-    sfree(top->idef.functype);
-    sfree(top->idef.iparams);
+    done_idef(&top->idef);
     done_block(&top->cgs);
     done_blocka(&top->excls);
-    for (int f = 0; f < F_NRE; f++)
-    {
-        sfree(top->idef.il[f].iatoms);
-    }
-    sfree(top->idef.iparams_posres);
-    sfree(top->idef.iparams_fbposres);
     done_atomtypes(&top->atomtypes);
 }
 

diff --git a/src/gromacs/topology/topology.h b/src/gromacs/topology/topology.h
index 5655e73d7a93f22ab901d7a42c57bf317e6f64fc..16eb265bd9f15b90471051dcd020b4ad36101ec1 100644 (file)
--- a/src/gromacs/topology/topology.h
+++ b/src/gromacs/topology/topology.h
@@ -182,6 +182,17 @@ void done_top(t_topology *top);
 // Frees both t_topology and gmx_mtop_t when the former has been created from
 // the latter.
 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
+/*! \brief
+ * Properly initialize local topology.
+ *
+ * \param[in] top Pointer to topology to initialize.
+ */
+void init_localtop(gmx_localtop_t *top);
+/*! \brief
+ * Properly clear up local topology,
+ *
+ * \param[in] top Pointer to topology to clear up.
+ */
 void done_localtop(gmx_localtop_t *top);
 void done_and_sfree_localtop(gmx_localtop_t *top);